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Merge discvr-24.11 to discvr-25.3 #45

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Merged
bbimber merged 10 commits into from
Mar 21, 2025
Merged

Merge discvr-24.11 to discvr-25.3 #45

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646c8bd
Back out change to WrappedColumn in favor of ExprColumn
bbimber Mar 20, 2025
3ca7188
Back out change to WrappedColumn in favor of ExprColumn
bbimber Mar 20, 2025
0a8df16
Fix date parsing
bbimber Mar 20, 2025
0be7f18
Fix typo
bbimber Mar 20, 2025
c6fa890
Restore lenient date parsing
bbimber Mar 20, 2025
14b1618
Misc code cleanup - improve generics (#230)
labkey-jeckels Mar 20, 2025
46d4ca6
Add workflow_dispatch
bbimber Mar 20, 2025
cfaea0d
Restore this for 24.11
bbimber Mar 20, 2025
a0ae29d
Merge pull request #44 from bimberlabinternal/24.11_fb_wrappedcol2
bbimber Mar 20, 2025
f10977f
Merge discvr-24.11 to discvr-25.3
bbimber Mar 20, 2025
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1 change: 1 addition & 0 deletions .github/workflows/build.yml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
name: Build DISCVR
on:
workflow_dispatch:
push:
pull_request:
jobs:
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15 changes: 7 additions & 8 deletions LDK/api-src/org/labkey/api/ldk/table/AbstractDataDefinedTable.java
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Expand Up @@ -57,15 +57,15 @@
* Date: 4/2/13
* Time: 2:54 PM
*/
abstract public class AbstractDataDefinedTable extends CustomPermissionsTable
abstract public class AbstractDataDefinedTable<SchemaType extends UserSchema> extends CustomPermissionsTable<SchemaType>
{
protected String _pk;

protected String _filterColumn;
protected String _filterValue;
protected String _valueColumn;

public AbstractDataDefinedTable(UserSchema schema, SchemaTableInfo table, ContainerFilter cf, String filterColumn, String valueColumn, String tableName, String filterValue)
public AbstractDataDefinedTable(SchemaType schema, SchemaTableInfo table, ContainerFilter cf, String filterColumn, String valueColumn, String tableName, String filterValue)
{
super(schema, table, cf);
_filterColumn = filterColumn;
Expand All @@ -77,23 +77,23 @@ public AbstractDataDefinedTable(UserSchema schema, SchemaTableInfo table, Contai
}

@Override
public CustomPermissionsTable init()
public CustomPermissionsTable<SchemaType> init()
{
super.init();

ColumnInfo col = getRealTable().getColumn(_filterColumn);
addCondition(col, _filterValue); //enforce only showing rows from this category

List<String> pks = getRealTable().getPkColumnNames();
assert pks.size() > 0;
assert !pks.isEmpty();
_pk = pks.get(0);

var valueCol = getMutableColumn(_valueColumn);
assert valueCol != null;

valueCol.setKeyField(true);
valueCol.setNullable(false);
getMutableColumn(_pk).setKeyField(false);
getMutableColumnOrThrow(_pk).setKeyField(false);

ColumnInfo filterCol = getColumn(_filterColumn);
assert filterCol != null;
Expand Down Expand Up @@ -135,7 +135,7 @@ protected class UpdateService extends SimpleQueryUpdateService
{
private final ValuesManager _vm;

public UpdateService(SimpleUserSchema.SimpleTable ti)
public UpdateService(SimpleUserSchema.SimpleTable<SchemaType> ti)
{
super(ti, ti.getRealTable());

Expand Down Expand Up @@ -217,8 +217,7 @@ public boolean testIfRowExists(String value)
{
boolean ret = _distinctValues.contains(value);

if (!_distinctValues.contains(value))
_distinctValues.add(value);
_distinctValues.add(value);

return ret;
}
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3 changes: 2 additions & 1 deletion LDK/api-src/org/labkey/api/ldk/table/ContainerScopedTable.java
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Expand Up @@ -287,7 +287,8 @@ public Object call()
Object pesudoPkVal = it.getInputColumnValue(inputColMap.get(_pseudoPk));
if (pesudoPkVal != null)
{
if (_context.getInsertOption() != QueryUpdateService.InsertOption.MERGE && keyManager.rowExists(c, pesudoPkVal))
// NOTE: this code is called for both inserts and updates:
if (_context.getInsertOption() == QueryUpdateService.InsertOption.INSERT && keyManager.rowExists(c, pesudoPkVal))
{
_context.getErrors().addRowError(new ValidationException("A record is already present with value: " + pesudoPkVal));
}
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6 changes: 5 additions & 1 deletion LDK/test/src/org/labkey/test/tests/external/labModules/LabModulesTest.java
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Expand Up @@ -16,12 +16,15 @@
package org.labkey.test.tests.external.labModules;

import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.DateFormatUtils;
import org.apache.commons.lang3.time.DateUtils;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.ss.usermodel.Workbook;
import org.junit.Assert;
import org.junit.Test;
import org.junit.experimental.categories.Category;
import org.labkey.api.util.DateUtil;
import org.labkey.remoteapi.CommandException;
import org.labkey.remoteapi.Connection;
import org.labkey.remoteapi.collections.CaseInsensitiveHashMap;
Expand Down Expand Up @@ -1415,6 +1418,7 @@ private void samplesTableTest() throws Exception
columnLabels.add(getColumnLabel(srr, name));
}

SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd");
List<List<String>> rows = new ArrayList<>();
for (Map<String, Object> row : srr.getRows())
{
Expand All @@ -1425,7 +1429,7 @@ private void samplesTableTest() throws Exception
String val = row.get(name) == null ? "" : String.valueOf(row.get(name));
if (name.toLowerCase().contains("date"))
{
val = StringUtils.isEmpty(val) ? "" : ExcelHelper.getDateTimeFormat().format(new Date(val));
val = StringUtils.isEmpty(val) ? "" : ExcelHelper.getDateTimeFormat().format(Date.parse(val));
}

target.add(val);
Expand Down
22 changes: 14 additions & 8 deletions laboratory/src/org/labkey/laboratory/query/LaboratoryTableCustomizer.java
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Expand Up @@ -19,7 +19,6 @@
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.TableCustomizer;
import org.labkey.api.data.TableInfo;
import org.labkey.api.data.WrappedColumnInfo;
import org.labkey.api.gwt.client.FacetingBehaviorType;
import org.labkey.api.laboratory.LaboratoryService;
import org.labkey.api.ldk.LDKService;
Expand Down Expand Up @@ -184,7 +183,8 @@ public void customizeColumns(AbstractTableInfo ti)
{
container.setHidden(true);

BaseColumnInfo wrappedContainer = WrappedColumnInfo.wrapAsCopy(ti, FieldKey.fromString("workbook"), container, "Workbook", null);
ExprColumn wrappedContainer = new ExprColumn(ti, FieldKey.fromString("workbook"), container.getValueSql(ExprColumn.STR_TABLE_ALIAS), container.getJdbcType(), container);
wrappedContainer.setLabel("Workbook");
wrappedContainer.setName("workbook");
wrappedContainer.setCalculated(true);
wrappedContainer.setShownInInsertView(false);
Expand Down Expand Up @@ -373,7 +373,8 @@ private void appendMajorEventsCol(final UserSchema us, AbstractTableInfo ds, fin
final String pkColSelectName = pk.getFieldKey().toSQLString();
final String pkColRawName = pk.getName();

BaseColumnInfo col = WrappedColumnInfo.wrapAsCopy(ds, FieldKey.fromString(name), pk, "Major Events", null);
BaseColumnInfo col = new ExprColumn(ds, FieldKey.fromString(name), pk.getValueSql(ExprColumn.STR_TABLE_ALIAS), pk.getJdbcType(), pk);
col.setLabel("Major Events");
col.setDescription("This column shows all major events recorded in this subject's history and will calculate the time elapsed between the current sample and these dates.");
col.setName(name);
col.setCalculated(true);
Expand Down Expand Up @@ -454,7 +455,8 @@ private void appendOverlapingProjectsCol(final UserSchema us, AbstractTableInfo
final String subjectSelectName = ds.getSqlDialect().makeLegalIdentifier(subjectColName);
final String dateSelectName = dateColName == null ? null : ds.getSqlDialect().makeLegalIdentifier(dateColName);

BaseColumnInfo col = WrappedColumnInfo.wrapAsCopy(ds, FieldKey.fromString(name), pk, "Overlapping Groups", null);
BaseColumnInfo col = new ExprColumn(ds, FieldKey.fromString(name), pk.getValueSql(ExprColumn.STR_TABLE_ALIAS), pk.getJdbcType(), pk);
col.setLabel("Overlapping Groups");
col.setDescription("This column shows all groups to which this subject belonged at the time of this sample.");
col.setName(name);
col.setCalculated(true);
Expand Down Expand Up @@ -503,7 +505,8 @@ public TableInfo getLookupTableInfo()

//add pivot column
String pivotColName = "overlappingProjectsPivot";
BaseColumnInfo col2 = WrappedColumnInfo.wrapAsCopy(ds, FieldKey.fromString(pivotColName), pk, "Overlapping Group List", null);
BaseColumnInfo col2 = new ExprColumn(ds, FieldKey.fromString(pivotColName), pk.getValueSql(ExprColumn.STR_TABLE_ALIAS), pk.getJdbcType(), pk);
col2.setLabel("Overlapping Group List");
col2.setName(pivotColName);
col2.setCalculated(true);
col2.setShownInInsertView(false);
Expand Down Expand Up @@ -572,7 +575,8 @@ public void appendProjectsCol(final UserSchema us, AbstractTableInfo ds, final S
final String publicTableName = ds.getPublicName();

final String colName = ds.getName() + "_allProjects";
BaseColumnInfo col = WrappedColumnInfo.wrapAsCopy(ds, FieldKey.fromString(name), pk, "Groups", null);
BaseColumnInfo col = new ExprColumn(ds, FieldKey.fromString(name), pk.getValueSql(ExprColumn.STR_TABLE_ALIAS), pk.getJdbcType(), pk);
col.setLabel("Groups");
col.setName(name);
col.setCalculated(true);
col.setShownInInsertView(false);
Expand Down Expand Up @@ -622,7 +626,8 @@ public TableInfo getLookupTableInfo()
//add pivot column
String pivotColName = "allProjectsPivot";
final String lookupName = ds.getName() + "_allProjectsPivot";
BaseColumnInfo col2 = WrappedColumnInfo.wrapAsCopy(ds, FieldKey.fromString(pivotColName), pk, "Group Summary List", null);
BaseColumnInfo col2 = new ExprColumn(ds, FieldKey.fromString(pivotColName), pk.getValueSql(ExprColumn.STR_TABLE_ALIAS), pk.getJdbcType(), pk);
col2.setLabel("Group Summary List");
col2.setName(pivotColName);
col2.setCalculated(true);
col2.setShownInInsertView(false);
Expand Down Expand Up @@ -772,7 +777,8 @@ private void appendRelativeDatesCol(final UserSchema us, AbstractTableInfo ds, f
final String pkColSelectName = pk.getFieldKey().toSQLString();
final String pkColRawName = pk.getName();

BaseColumnInfo col = WrappedColumnInfo.wrapAsCopy(ds, FieldKey.fromString(name), pk, "Relative Dates", null);
BaseColumnInfo col = new ExprColumn(ds, FieldKey.fromString(name), pk.getValueSql(ExprColumn.STR_TABLE_ALIAS), pk.getJdbcType(), pk);
col.setLabel("Relative Dates");
col.setName(name);
col.setCalculated(true);
col.setShownInInsertView(false);
Expand Down